[gmx-users] no domain decomposition

[Chandan Choudhury]

Hi!

Sometime decreasing the total number of nodes serves the purpose. Did you
try decreasing the total number of nodes?

Chandan

On Sun, Sep 27, 2015 at 8:00 PM, soumadwip ghosh <soumadwipghosh at gmail.com>
wrote:

> Hi all,
>          I am simulating a DNA encapsulated in a carbon nanotube in the
> presence of some fillers. Previously I was having this domain decomposition
> error every time I was attempting an mdrun. There were some problems in the
> initial structure which I fixed according to the suggestion of Justin and
> Tsjerk and now energy minimization and position restrained dynamics are all
> going well. Today, I took the npt.gro file and tried the production run
> with the following mdp file..
>
> title = dna in water
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 50000000              ;2 * 25000000 = 50000 ps, 50 ns
> dt              = 0.001         ; 2 fs
> ; Output control
> nstxout         = 1000          ; save coordinates every 2 ps
> nstvout         = 1000          ; save velocities every 2 ps
> nstxtcout       = 1000          ; xtc compressed trajectory output every 2
> ps
> nstenergy       = 1000          ; save energies every 2 ps
> nstlog          = 1000          ; update log file every 2 ps
> ; Bond parameters
> continuation    = yes           ; Restarting after NPT
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> cutoff-scheme   = Verlet        ; search neighboring grid cells
> vdwtype         = cutoff        ; 10 fs
> vdw-modifier    = force-switch
> rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
> rvdw            = 1.2           ; short-range electrostatic cutoff (in nm)
> rvdw-switch     = 1.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME
> rcoulomb        = 1.2           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = SYSTEM        ; two coupling groups - more accurate
> tau_t           = 0.1           ; time constant, in ps
> ref_t           = 300           ; reference temperature, one for each
> group, in K
> ; Pressure coupling is on
> pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
> pcoupltype      = isotropic     ; uniform scaling of box vectors
> tau_p           = 2.0           ; time constant, in ps
> ref_p           = 1.0           ; reference pressure, in bar
> compressibility = 4.5e-5        ; isothermal compressibility of water,
> bar^-1
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = no            ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = no            ; Velocity generation is off
> energygrps      = UNK a1 t2 c3 g4 LIG
>
> I obtained the tpr file using grompp but my mdrun crashed telling,
> A charge group moved too far between two domain decomposition step
> which means your system is not well equilibrated.
>
> Then I checked the pressure and temperature of the npt.edr file and the
> pressure value was
>
> 0.67 with an error bar of 0.97 while the desired pressure was 1.0 bar. Is
> this the reason why mdrun is crashing? I have done NPT for 10 ns and still
> the pressure has not converged. What is going wrong here ? I am using
> gromacs 5.0.5 in combination with CHARMM 27 force field.
>
> As far as I understand my system is not equilibrated properly. Should I
> perform NPT for a longer time and see whether the pressure is getting
> converged or the problem is something else?
>
> Any kind of help would be appreciated.
>
> Thanks and regards,
> Soumadwip Ghosh
> Research Fellow,
> IITB
> Mumbai
> India
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-- 

Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India

*"All work and no play makes Jack a dull boy...”*